I am really enjoying my course on Atheism! We are talking about how the roots of most modern atheist beliefs go back to the 13/14th century, with the conceptualization of God as primarily will (as opposed to reason, which was the characteristic most theologians focused on from the time of Augustine to medieval scholasticism). As a result (centuries later, through much history), humans have come to understand themselves also more in terms of will than reason - we identify freedom not as the ability to reason what is right and choose whether or not to do that, but as the ability to decide what is right. This becomes a problem because if we allow that God decides what is right, our human freedom is limited and we're not much better than slaves. God seems arbitrary and mean, and obeying him is humiliating (and sexually repressive). This is pretty much Christopher Hitchens' definition of religion.
This is not what Christianity is to me though, and it's not what the Bible says, and it's not what centuries of Christian theology say. So most atheists are up in arms against ideas about God that Christians don't even believe. The issue of will and freedom is complicated, but the main point is that when God gave us free will it wasn't a trick. We are free to make whatever choices we want. But our will has limits - we control our conduct in the world, but we can't change how the world works.
Science works because we understand that the earth is subject to physical laws - tons of math. Christianity says that the same God who made the world in such a beautiful and rational way (fallen though it may be) is responsible for moral laws as well. We have free will, so we can break these moral laws (knowingly or unknowingly), but we cannot change the fact they exist. And these laws are not arbitrary style-crampers; they are in fact necessary for human life to flourish. Just as the earth needs to be a certain distance from the sun and travel at a certain velocity through space, spouses must be faithful to each other and neighbours cannot kill each other, or everything goes wrong. Okay, so the results are not as immediate and drastic and widespread when a family breaks up as when a meteor strikes the earth off its course (thank you Hollywood for umpteen visuals of that). But God's moral law is designed for the good of human life, just as his laws of physics also sustain life.
In 1 Corinthians 13:11-12, Paul writes, " When I was a child, I spoke and thought and reasoned as a child. But when I grew up, I put away childish things. Now we see things imperfectly as in a cloudy mirror, but then we will see everything with perfect clarity. All that I know now is partial and incomplete, but then I will know everything completely, just as God now knows me completely."
Yes, there are still unanswered questions in science and ethics... but that doesn't mean the answers don't exist. Faith is required to believe that perfect clarity will one day come, but it is not an irrational, brainwashing faith. It is a hope based in the love and goodness of a God who has brought us this far and who responds when we seek him. The rational basis for morality isn't always clear, but faith tells us it is there even when our rationality cannot prove it. As Christians, we don't give up our free will, but we submit it to God and ask for his help. Maybe atheists would say it's the same thing, but it's really not.